Detection and characterization of single SARS-CoV-2 viral particles by flow virometry

Virus infected cells release viral particles, which have variable protein content and are functionally diverse. Deciphering this heterogeneity remains a challenge. Here, we adapt flow virometry to detect and phenotype severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) particles. In supernatants of infected cells, we observe particles measuring 70–100 nm. The appearance of these particles is associated to the increase in viral RNA and infectivity. Sample inactivation using temperature or detergent leads to the disappearance of these particles. Using antibodies and dyes for lipid membranes and nucleic acids, we detect the spike protein, the lipid envelope and the RNA genome. We further confirm the presence of viral particles by electron microscopy. Analyzing different viral preparations demonstrate that spike detection in particles outcompetes particle concentration to predict infectivity. Antibodies against different spike epitopes enable probing of spike conformation changes in the presence of soluble ACE2. Lastly, we detect SARS-CoV-2 particles in PCR-confirmed patient nasal swabs without prior purification steps. In summary, we developed an efficient framework to detect and characterize single SARS-CoV-2 particles.